[English] 日本語
Yorodumi
- PDB-6j1r: Crystal structure of Candida Antarctica Lipase B mutant - RR -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6j1r
TitleCrystal structure of Candida Antarctica Lipase B mutant - RR
ComponentsLipase B
KeywordsHYDROLASE / CALB
Function / homology
Function and homology information


triacylglycerol lipase / triacylglycerol lipase activity / lipid catabolic process
Similarity search - Function
: / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Lipase B
Similarity search - Component
Biological speciesPseudozyma antarctica (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.601 Å
AuthorsCen, Y.X. / Zhou, J.H. / Wu, Q.
CitationJournal: J.Am.Chem.Soc. / Year: 2019
Title: Stereodivergent Protein Engineering of a Lipase To Access All Possible Stereoisomers of Chiral Esters with Two Stereocenters.
Authors: Xu, J. / Cen, Y. / Singh, W. / Fan, J. / Wu, L. / Lin, X. / Zhou, J. / Huang, M. / Reetz, M.T. / Wu, Q.
History
DepositionDec 29, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 1, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Lipase B
A: Lipase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,42812
Polymers66,6272
Non-polymers80110
Water5,783321
1
B: Lipase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7026
Polymers33,3141
Non-polymers3885
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12090 Å2
MethodPISA
2
A: Lipase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7266
Polymers33,3141
Non-polymers4125
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-18 kcal/mol
Surface area11870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.023, 80.670, 73.646
Angle α, β, γ (deg.)90.00, 98.48, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Lipase B / CALB


Mass: 33313.590 Da / Num. of mol.: 2 / Mutation: T57A, A89T, Q157L, I189A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudozyma antarctica (fungus) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P41365, triacylglycerol lipase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.03 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2M lithium sulfate 0.1M Tris 7.5 30% PEG3000 3% 2-methyl-2,4-pentadiol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 70816 / % possible obs: 99 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 20.977
Reflection shellResolution: 1.6→1.63 Å / Rmerge(I) obs: 0.666 / Mean I/σ(I) obs: 2.636 / Num. unique obs: 3349

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TCA

1tca


Resolution: 1.601→46.509 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.29
RfactorNum. reflection% reflection
Rfree0.2151 3340 5.1 %
Rwork0.1763 --
obs0.1782 65549 91.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.601→46.509 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4658 0 47 321 5026
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0184959
X-RAY DIFFRACTIONf_angle_d1.566824
X-RAY DIFFRACTIONf_dihedral_angle_d17.3711794
X-RAY DIFFRACTIONf_chiral_restr0.115787
X-RAY DIFFRACTIONf_plane_restr0.01899
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6012-1.6240.29391070.21141688X-RAY DIFFRACTION60
1.624-1.64830.2317980.19541875X-RAY DIFFRACTION67
1.6483-1.6740.26541070.19081999X-RAY DIFFRACTION70
1.674-1.70150.24991220.19222099X-RAY DIFFRACTION76
1.7015-1.73080.24961190.21812269X-RAY DIFFRACTION79
1.7308-1.76230.23931220.20732317X-RAY DIFFRACTION82
1.7623-1.79620.27691340.20982380X-RAY DIFFRACTION84
1.7962-1.83290.25121100.1892510X-RAY DIFFRACTION90
1.8329-1.87270.2221550.19032784X-RAY DIFFRACTION98
1.8727-1.91630.22361370.18582789X-RAY DIFFRACTION99
1.9163-1.96420.21981580.18662827X-RAY DIFFRACTION100
1.9642-2.01730.251560.18662821X-RAY DIFFRACTION100
2.0173-2.07670.22131510.1872800X-RAY DIFFRACTION100
2.0767-2.14370.21751220.18882849X-RAY DIFFRACTION99
2.1437-2.22030.21391790.17522755X-RAY DIFFRACTION99
2.2203-2.30920.22041630.16782789X-RAY DIFFRACTION100
2.3092-2.41430.19891520.17672835X-RAY DIFFRACTION100
2.4143-2.54160.23611260.18052868X-RAY DIFFRACTION100
2.5416-2.70080.23731560.17982801X-RAY DIFFRACTION99
2.7008-2.90930.23211600.19292794X-RAY DIFFRACTION98
2.9093-3.2020.23981660.20032815X-RAY DIFFRACTION100
3.202-3.66520.20361470.17992837X-RAY DIFFRACTION100
3.6652-4.61710.16261410.13662833X-RAY DIFFRACTION99
4.6171-46.52860.16391520.13692875X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -75.1514 Å / Origin y: 19.0727 Å / Origin z: 106.1914 Å
111213212223313233
T0.1087 Å20.0194 Å20.0979 Å2-0.0363 Å2-0.0016 Å2--0.0679 Å2
L0.5281 °20.368 °20.4292 °2-0.6301 °20.3486 °2--0.5152 °2
S0.1306 Å °-0.0762 Å °-0.0907 Å °0.0564 Å °-0.0257 Å °-0.0732 Å °0.1138 Å °-0.0808 Å °-0.0312 Å °
Refinement TLS groupSelection details: all

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more